Pôle Scientifique de Modélisation Numérique (PSMN)

All nf-core pipelines have been successfully configured for use on the tars cluster at the Institut Pasteur.

To use, run the pipeline with -profile pasteur. This will download and launch the psmn.config which has been pre-configured with a setup suitable for the PSMN cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.

Running the workflow on the PSMN cluster

Install Nextflow and Charliecloud

The Nextflow binary is available in the folder /Xnfs/abc/nextflow_bin/. All the Charliecloud binaries are available in the folder Xnfs/abc/charliecloud_bin/.

You can update your $PATH variable with the following command to have access to Nextflow and Charliecloud:

PATH=/Xnfs/abc/charliecloud_bin/:/Xnfs/abc/nextflow_bin/:$PATH
PATH=/Xnfs/abc/charliecloud_bin/:/Xnfs/abc/nextflow_bin/:$PATH

or add this line to your ~/.zshrc or ~/.bashrc configuration file.

Install nf-core

nf-core is available on the PSMN as a Charliecloud container you can run the classical nf-core command by prefixing them with:

ch-run -b /scratch:/scratch /Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core
ch-run -b /scratch:/scratch /Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core

For exemple to download the nf-core/rnaseq pipeline you can use the command:

ch-run -b /scratch:/scratch \
  /Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core \
  download rnaseq -r 3.9 --outdir nf-core-rnaseq
ch-run -b /scratch:/scratch \
  /Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core \
  download rnaseq -r 3.9 --outdir nf-core-rnaseq

Download and launch a nf-core pipeline

You can use the nf-core download command to download an nf-core pipeline and the configuration files for the PSMN:

cd <your scratch directory>
ch-run -b /scratch:/scratch \
  /Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core \
  download rnaseq -r 3.9 --outdir <your scratch directory>/nf-core-rnaseq -x none -c none

The you can launch this pipeline with the PSMN profile

tmux
cd nf-core-rnaseq
nextflow run workflow -profile test,psmn --outdir results/

Config file

See config file on GitHub

psmn.config
//Profile config names for nf-core/configs
params {
  config_profile_description = 'PSMN (Pôle Scientifique de Modélisation Numérique) HPC cluster profile'
  config_profile_contact = 'Laurent Modolo (@l-modolo)'
  config_profile_url = 'http://www.ens-lyon.fr/PSMN/doku.php?id=en:accueil'
}
 
charliecloud {
  enabled = true
  cacheDir = "/Xnfs/abc/charliecloud"
  runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
  readOnlyInputs = true
}
 
process {
  executor = 'slurm'
  clusterOptions = "--partition=Lake"
}
 
params {
  max_memory = 512.GB
  max_cpus = 32
  max_time = 24.h
}
 
psmn.config
//Profile config names for nf-core/configs
params {
  config_profile_description = 'PSMN (Pôle Scientifique de Modélisation Numérique) HPC cluster profile'
  config_profile_contact = 'Laurent Modolo (@l-modolo)'
  config_profile_url = 'http://www.ens-lyon.fr/PSMN/doku.php?id=en:accueil'
}
 
charliecloud {
  enabled = true
  cacheDir = "/Xnfs/abc/charliecloud"
  runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
  readOnlyInputs = true
}
 
process {
  executor = 'slurm'
  clusterOptions = "--partition=Lake"
}
 
params {
  max_memory = 512.GB
  max_cpus = 32
  max_time = 24.h
}